cgob/codonDT_snakemake

Code running to completion, but not producing output files

agoldkamp opened this issue · 4 comments

agoldkamp commented

Hello, I am currently using codonDT_snakemake to analyze my ribosome profiling data. The code will run without any errors and finish, but I am unable to find any output files. I am assuming the output files should be within the /Data/ directory? Any suggestions on how I can resolve this?

Screen Shot 2022-01-13 at 1 50 13 PM

cgob commented

Hello,
Do you get any folders or files created in the "workdir" directory that you defined in the "config.yaml" file?

Cédric

agoldkamp commented

Hi,
I am not getting any folders or files created in the working directory. I just redownloaded. I initially got this error, so I had added "/Cow/genome" within the "references" directory. I am assuming this is what is causing the issue because I believe the program should generate these folders on its own?

Screen Shot 2022-01-14 at 3 40 56 PM

agoldkamp commented

Hi again,

It looks like the error was on my end. I ran the default data set which successfully ran and produced output files. I then added my fastq files to the "Data/Raw" directory, and removed the --touch command and it started to produce output files.

However, it failed for one of the samples (Liver_2) at the "findAsite" step.

Screen Shot 2022-01-17 at 12 06 20 PM

I apologize for all of the questions. I think this tool could be very beneficial for our project and appreciate any feedback!

Thank you,
Anna

cgob commented

Dear Anna,

Sorry for the late reply. Did you solve your issue ? Were you able to run the pipeline on your data successfully?

Best,

Cédric